[phenixbb] mutate to polyAla

Nathaniel Echols NEchols at lbl.gov
Thu May 14 09:02:42 PDT 2009

On May 14, 2009, at 4:48 AM, Schubert, Carsten [PRDUS] wrote:
> Sometimes truncation/mutation  to poly-gly or poly-Ser is desirable.  
> If not already present could this be another option? Another  
> interesting option would be to be able to change OR keep the residue  
> names of the template to be mutated. Sometimes it is useful to chop  
> the sidechains, but still be able to tell what residue this is  
> supposed to be via the residue name. Again some of this may already  
> be present, haven’t had a chance to play around with this.

None of this actually changes the atom names - I just looked at the  
pdbtools source code and it only deletes atoms after Cbeta.   
Specifying an atom selection to keep can also be used for poly-Gly or  

> phenix.pdbtools model.pdb keep="backbone"
> phenix.pdbtools model.pdb remove="sidechain"

. . . these will actually get rid of Cbeta too, so poly-Gly, and

phenix.pdbtools model.pdb keep="backbone or name cb or name cg or name  
cg1 or name og1 or name sg1"

will chop off everything but the beta and gamma positions (without  
branching).  Smaller residues will be untouched.  I don't think  
there's a simple way to actually change the identity of every residue  
in phenix/cctbx, but I've found that this usually just creates  
problems anyway.

I'm working on a graphical frontend to pdbtools - it may take another  
week or two for it to be usable, but it will make all of this  
relatively easy, I hope.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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